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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:44, 17 September 2013


Full id: C1405_smallcell_pineal_small_occipital_somatostatinoma_medial_amygdala



Phase1 CAGE Peaks

Hg19::chr15:51973680..51973707,+p1@SCG3
Hg19::chr15:51973708..51973725,+p3@SCG3
Hg19::chr1:154540296..154540327,+p1@CHRNB2
Hg19::chr1:42846443..42846502,+p1@RIMKLA
Hg19::chr20:17207640..17207661,+p2@PCSK2
Hg19::chr2:220408724..220408789,+p1@TMEM198


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

GO IDGO nameFDR corrected p-value
GO:0004286proprotein convertase 2 activity0.00588650804177389
GO:0014059regulation of dopamine secretion0.00588650804177389
GO:0021955central nervous system neuron axonogenesis0.00588650804177389
GO:0014046dopamine secretion0.00588650804177389
GO:0021952central nervous system projection neuron axonogenesis0.00588650804177389
GO:0032225regulation of synaptic transmission, dopaminergic0.00588650804177389
GO:0048814regulation of dendrite morphogenesis0.00588650804177389
GO:0016808proprotein convertase activity0.00588650804177389
GO:0050433regulation of catecholamine secretion0.00588650804177389
GO:0050773regulation of dendrite development0.00588650804177389
GO:0050432catecholamine secretion0.00588650804177389
GO:0048813dendrite morphogenesis0.00588650804177389
GO:0035094response to nicotine0.00588650804177389
GO:0008306associative learning0.00588650804177389
GO:0021954central nervous system neuron development0.00588650804177389
GO:0001963synaptic transmission, dopaminergic0.00727114064039783
GO:0021953central nervous system neuron differentiation0.00727114064039783
GO:0043279response to alkaloid0.00784706013717014
GO:0030890positive regulation of B cell proliferation0.00784706013717014
GO:0051899membrane depolarization0.00784706013717014
GO:0030888regulation of B cell proliferation0.00784706013717014
GO:0007613memory0.00784706013717014
GO:0014070response to organic cyclic substance0.00784706013717014
GO:0007267cell-cell signaling0.00784706013717014
GO:0016358dendrite development0.00784706013717014
GO:0046928regulation of neurotransmitter secretion0.00784706013717014
GO:0007271synaptic transmission, cholinergic0.00784706013717014
GO:0005892nicotinic acetylcholine-gated receptor-channel complex0.00819713399072745
GO:0050804regulation of synaptic transmission0.00962878184772167
GO:0007612learning0.00962878184772167
GO:0051969regulation of transmission of nerve impulse0.00962878184772167
GO:0050871positive regulation of B cell activation0.00962878184772167
GO:0042100B cell proliferation0.00962878184772167
GO:0007270nerve-nerve synaptic transmission0.00986449096606127
GO:0015464acetylcholine receptor activity0.0105907245387965
GO:0042166acetylcholine binding0.0107865314738784
GO:0004889nicotinic acetylcholine-activated cation-selective channel activity0.010971726164849
GO:0031644regulation of neurological process0.0113135441234759
GO:0050864regulation of B cell activation0.0113135441234759
GO:0032946positive regulation of mononuclear cell proliferation0.0129120955954723
GO:0050671positive regulation of lymphocyte proliferation0.0129120955954723
GO:0042391regulation of membrane potential0.0130244367204868
GO:0046879hormone secretion0.0139514273861003
GO:0004289subtilase activity0.0140349464792311
GO:0050767regulation of neurogenesis0.0148980047794665
GO:0007269neurotransmitter secretion0.0153402913403732
GO:0050670regulation of lymphocyte proliferation0.0154352590373835
GO:0032944regulation of mononuclear cell proliferation0.0154352590373835
GO:0043176amine binding0.0155225462346516
GO:0007611learning and/or memory0.0155225462346516
GO:0001666response to hypoxia0.016599698156691
GO:0009897external side of plasma membrane0.0166898725144052
GO:0051251positive regulation of lymphocyte activation0.0166898725144052
GO:0045055regulated secretory pathway0.0166898725144052
GO:0032943mononuclear cell proliferation0.0166898725144052
GO:0046651lymphocyte proliferation0.0166898725144052
GO:0051046regulation of secretion0.018250114138437
GO:0042113B cell activation0.0185263443156412
GO:0010033response to organic substance0.0185263443156412
GO:0003001generation of a signal involved in cell-cell signaling0.0205633800705441
GO:0005231excitatory extracellular ligand-gated ion channel activity0.0208029434278018
GO:0051249regulation of lymphocyte activation0.0216019449595088
GO:0001505regulation of neurotransmitter levels0.0218172203414233
GO:0050865regulation of cell activation0.0220257035271641
GO:0043235receptor complex0.0297930673958638
GO:0007409axonogenesis0.0304050423764427
GO:0048667neuron morphogenesis during differentiation0.0310584828125304
GO:0048812neurite morphogenesis0.0310584828125304
GO:0000904cellular morphogenesis during differentiation0.0321330951278089
GO:0005230extracellular ligand-gated ion channel activity0.0329261050180939
GO:0031175neurite development0.0334496300870671
GO:0030594neurotransmitter receptor activity0.0344449617093647
GO:0042165neurotransmitter binding0.0349327699114972
GO:0009986cell surface0.0349350746353671
GO:0045211postsynaptic membrane0.0349350746353671
GO:0048666neuron development0.0353916510545207
GO:0046649lymphocyte activation0.0353916510545207
GO:0044456synapse part0.0360328383118421
GO:0015276ligand-gated ion channel activity0.0360328383118421
GO:0022834ligand-gated channel activity0.0360328383118421
GO:0045321leukocyte activation0.0390415637659016
GO:0006816calcium ion transport0.0392047360730927
GO:0032990cell part morphogenesis0.0421350544475285
GO:0048858cell projection morphogenesis0.0421350544475285
GO:0030030cell projection organization and biogenesis0.0421350544475285
GO:0001775cell activation0.0423697106789525
GO:0030182neuron differentiation0.0423697106789525
GO:0007601visual perception0.0439646645802476
GO:0050953sensory perception of light stimulus0.0439646645802476
GO:0008284positive regulation of cell proliferation0.0442068515711884
GO:0007417central nervous system development0.0442068515711884
GO:0050793regulation of developmental process0.0442068515711884
GO:0055082cellular chemical homeostasis0.0442068515711884
GO:0006873cellular ion homeostasis0.0442068515711884
GO:0045045secretory pathway0.0442068515711884
GO:0048699generation of neurons0.0442068515711884
GO:0015674di-, tri-valent inorganic cation transport0.0446484715958753
GO:0022008neurogenesis0.0468559071508107
GO:0050801ion homeostasis0.0472608049517232
GO:0051239regulation of multicellular organismal process0.0485262389823197



Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br>disease_data<br>

Cell Type
Ontology termp-valuen
neuronal stem cell2.69e-088
Uber Anatomy
Ontology termp-valuen
adult organism1.33e-60114
nervous system7.62e-5689
central nervous system1.22e-5381
neural tube2.51e-5056
neural rod2.51e-5056
future spinal cord2.51e-5056
neural keel2.51e-5056
regional part of nervous system1.22e-4753
regional part of brain1.22e-4753
neurectoderm4.12e-4386
brain5.73e-4268
future brain5.73e-4268
regional part of forebrain2.01e-4141
forebrain2.01e-4141
anterior neural tube2.01e-4141
future forebrain2.01e-4141
neural plate1.75e-4082
presumptive neural plate1.75e-4082
ectoderm-derived structure3.46e-35171
ectoderm3.46e-35171
presumptive ectoderm3.46e-35171
organ system subdivision4.90e-35223
telencephalon1.27e-3434
brain grey matter1.61e-3434
gray matter1.61e-3434
cerebral hemisphere4.19e-3332
ecto-epithelium1.21e-32104
regional part of telencephalon1.22e-3232
pre-chordal neural plate9.98e-3261
cerebral cortex3.86e-2625
pallium3.86e-2625
regional part of cerebral cortex2.27e-2522
structure with developmental contribution from neural crest8.45e-24132
neocortex1.76e-2320
anatomical cluster8.57e-20373
tube6.77e-12192
multi-tissue structure9.79e-12342
embryo1.13e-10592
organ part1.91e-10218
posterior neural tube3.61e-1015
chordal neural plate3.61e-1015
anatomical conduit4.78e-10240
basal ganglion5.86e-109
nuclear complex of neuraxis5.86e-109
aggregate regional part of brain5.86e-109
collection of basal ganglia5.86e-109
cerebral subcortex5.86e-109
neural nucleus9.72e-109
nucleus of brain9.72e-109
developing anatomical structure9.17e-09581
segmental subdivision of nervous system1.73e-0813
temporal lobe2.04e-086
organ3.08e-08503
diencephalon4.21e-087
future diencephalon4.21e-087
gyrus5.23e-086
telencephalic nucleus6.22e-087
multi-cellular organism8.10e-08656
segmental subdivision of hindbrain8.92e-0812
hindbrain8.92e-0812
presumptive hindbrain8.92e-0812
embryonic structure1.74e-07564
germ layer1.80e-07560
germ layer / neural crest1.80e-07560
embryonic tissue1.80e-07560
presumptive structure1.80e-07560
germ layer / neural crest derived structure1.80e-07560
epiblast (generic)1.80e-07560
parietal lobe4.71e-075
brainstem5.59e-076
occipital lobe5.67e-075
epithelium9.67e-07306
Disease
Ontology termp-valuen
neuroectodermal tumor7.47e-0910
germ cell and embryonal cancer5.69e-0822
germ cell cancer5.69e-0822


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.14.08206
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.12.03395
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.11.05129
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.906394
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.808182
MA0056.10
MA0057.11.41984
MA0058.10.458909
MA0059.10.457555
MA0060.12.08473
MA0061.11.93637
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.578694
MA0069.11.02175
MA0070.11.01032
MA0071.11.51422
MA0072.11.00572
MA0073.10.216116
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.32124
MA0089.10
MA0090.10.490736
MA0091.12.36274
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.11.02896
MA0103.10.381434
MA0105.11.34409
MA0106.10.70837
MA0107.10.857383
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.865577
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.641617
MA0140.10.622527
MA0141.11.15452
MA0142.10.838805
MA0143.10.725558
MA0144.10.811435
MA0145.11.16614
MA0146.11.8938
MA0147.10.327615
MA0148.10.584698
MA0149.11.48729
MA0062.21.22729
MA0035.20.621793
MA0039.21.47843
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.21.12726
MA0065.20.718489
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.11.3291
MA0155.10.65596
MA0156.11.07131
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.12.97671
MA0163.10.813808
MA0164.10.738243
MA0080.21.02158
MA0018.21.69036
MA0099.20.629739
MA0079.23.22572
MA0102.21.58513
MA0258.10.289793
MA0259.10.336472
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
BCL3#602211.51570093457940.01162725346801640.0424801904759729
HDAC2#306636.707810118313130.006973940027962660.029487907796777
JUND#372744.663109294580680.004917643408260230.0229888438259384
NRF1#489936.105139723855450.009090162079396740.0344048502359251
POLR2A#543062.147453176558070.01019570676818780.0380187596102102
REST#597858.041690596773356.54774545315482e-050.00106153366560391
SIN3A#2594254.507403939012610.001096110061208640.00765986207310597
SMARCA4#6597252.25530110262930.0005995659215741950.00500984601034381
SMARCB1#659839.126357890578710.002900247150367020.0156779975226284
SRF#672236.89858913108390.00644245168930370.0280001336653845
TAF1#687263.343046285745290.0007162474284635620.00573080251140014
TAF7#687935.716534702461960.01092729379889660.0402112553138706
ZNF263#1012745.481227758007120.002675609380607230.014745288802767



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

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